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- PDB-1zsr: Crystal structure of wild type HIV-1 protease (BRU isolate) with ... -

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Basic information

Entry
Database: PDB / ID: 1zsr
TitleCrystal structure of wild type HIV-1 protease (BRU isolate) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / PROTEASE / PEPTIDOMIMETIC INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2 / Chem-0ZT / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSkalova, T. / Dohnalek, J. / Duskova, J. / Petrokova, H. / Hasek, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 A resolution.
Authors: Duskova, J. / Dohnalek, J. / Skalova, T. / Petrokova, H. / Vondrackova, E. / Hradilek, M. / Konvalinka, J. / Soucek, M. / Brynda, J. / Fabry, M. / Sedlacek, J. / Hasek, J.
History
DepositionMay 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3433
Polymers21,6402
Non-polymers7041
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-26 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.801, 62.801, 82.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10819.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pT7Q10H1N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03367, UniProt: P03366*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-0ZT / N-{(2S,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 703.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H49N5O8 / References: BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR 0ZT IS A PSEUDOPEPTIDE WITH THE HYDROXYETHYAMINE ISOSTERE IN THE S CONFIGURATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 1 M Ammonium Phosphate, 0.1 M Na Citrate, 3 mg/ml protein, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1997
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→40 Å / Num. all: 10981 / Num. obs: 10981 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -999 / Redundancy: 6.98 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 26.7
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.98 / Num. unique all: 553 / Rsym value: 0.305 / % possible all: 69.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IIQ

1iiq


Resolution: 2.06→40 Å / Isotropic thermal model: Isotropic / Cross valid method: R-FREE statistic throughout / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used maximum likelihood refinement procedure against F values. The classical crystallographic residual used as target function in the final refinement cycle.
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 545 -RANDOM
Rwork0.2023 ---
all0.1936 10960 --
obs0.1936 10960 96 %-
Solvent computationSolvent model: Jiang & Brunger, 1994 / Bsol: 101.4 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.197 Å2-0.508 Å20 Å2
2---0.197 Å20 Å2
3---0.393 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.06→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 51 152 1721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010709
X-RAY DIFFRACTIONc_angle_deg1.65036
X-RAY DIFFRACTIONc_mcbond_it2.081
X-RAY DIFFRACTIONc_mcangle_it3.275
X-RAY DIFFRACTIONc_scbond_it3.874
X-RAY DIFFRACTIONc_scangle_it5.786
LS refinement shellResolution: 2.06→2.15 Å
RfactorNum. reflection
Rfree0.2887 26
Rwork0.2407 -
obs-985

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